Retracing an insect pest invasion route

Next Monday, Emilie will present a paper presenting a study aiming to search for the most likely invasion route of an insect pest species: the aphid Myzus persicae nicotianae. They used seven microsatellites and various methods combining traditional (F-statistics, genetic diversity parameters), Bayesian-based (Structure) and coalescent-based (DiyABC) approaches. These methods helped them first to identify the genetic subdivisions of the species between the potential sources in Europe and North America and the newly colonized areas (South America). Then, the program DiyABC was used to test different colonization scenarios. Thanks Emilie.

From Zepeda-Paulo FA, Simon JC, Ramirez CC, Fuentes-Contreras E, Margaritopoulos JT, Wilson ACC, Sorenson CE, Briones LM, Azevedo R, Ohashi DV, Lacroix C, Glais L, Figueroa CC (2010) Molecular Ecology 19, 4738–4752

Title: The invasion route for an insect pest species: the tobacco aphid in the New World

Abstract

Background. Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species.

Aims. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile.

Major results and conclusions. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and ⁄ or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or ‘superclones’ in asexually reproducing organisms.

Development of microsatellite markers in the Sparidae and their application in population genetics of the hottentot seabream around South Africa

By defining the degree of genetic spatial variation of populations, inferences can be made about what biological and environmental factors influence the genetic divergence and biogeography of marine species (Cowen et al. 2006). The marine environment is extensive, covering over 70 percent of the earth’s surface and contain highly diverse habitats (Avise 1998; Chopelet et al. 2009). These habitats are not always continuous and may be patchy (e.g. kelp beds) and variable (Gratwicke & Speight 2005). The interactions of individuals (life-history traits) of a species within and between patchy habitats leads to a specific degree of genetic diversity and population structure that can be identified (Chopelet et al. 2009). Marine species are often characterised by specific life-history traits such as high fecundity, numerous pelagic eggs and larvae, mobility and longevity which contribute to high levels of gene flow counterbalancing spatial heterogeneity of habitats (Avise 1998; Hauser & Carvalho 2008). These life-history traits coupled with homogenous transient habitats (allowing dispersal between habitats) that have limited physical barriers lead to a general lack of highly divergent populations at a regional scale. This is however not always the case for all organisms with several marine fish having been identified with population structure on local and regional scales (González et al. 2008; Narum et al. 2008; Nielsen et al. 2009). Population genetics plays a major role in the management and the conservation of commercial marine fish as the statistical approaches allow for the identification of the number of stocks that may need to be conserved separately. Marine fish are harvested in large quantities and this has led to overexploitation (Carvalho & Hauser 1998). By over-harvesting, genetic diversity may be lost which has wider implications as this decreases the ability of the species to adapt (Fenberg & Roy 2008). Also marine fish are one of the last wild sources of protein and as the stocks become depleted it has far reaching implications on the people who rely on it as a food source and income (Ryman et al. 1995). The correct management and conservation required to maintain the sustainability of this resource starts with the improvement of knowledge of the population biology of the targeted species.

South Africa has a wide range of marine fish species due to the diverse geological and oceanographic features which provide a number of habitats along the coast. One of the most prevalent and diverse fish families along the South African coast is the Sparidae. This family is of economic importance to the line fishery and many of these species are considered vulnerable or endangered due to a combination of overfishing and life-history traits. Two species of particular interest are the hottentot seabream (Pachymetopon blochii) and white steenbras (Lithognathus lithognathus). Both species are endemic to southern Africa and are considered vulnerable to overexploitation.

This study reports the development of microsatellite markers for both the above mentioned species using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) developed by Zane et al. (2002). Nine polymorphic markers were identified in each of these species. Nineteen markers (fifteen newly developed and four from other sparids) were used as a panel on eleven economically important sparids, to test microsatellite cross-species amplification. From this study twelve adequate polymorphic loci were identified for the white steenbras (applied in a population genetic study by a PhD student associated with SAIAB) and fourteen in the hottentot seabream which were applied in this dissertation. We were also able to identify a number of polymorphic loci for the other sparids (Fig. 1). It was concluded that the sparids do not show a negative correlation between genetic distance and microsatellite amplification success and polymorphism.

Fig. 1 Summary of the number of microsatellites that amplification (A) and were polymorphic (P) in the different sparid species included in this study.

The study further investigated the population genetic structure of the hottentot seabream. Pachymetopon blochii is an endemic, demersal sparid occurring along the west coast of southern Africa, found mainly in kelp beds and rocky outcrops (Heemstra & Heemstra 2004). This species is targeted by line fisheries and is considered vulnerable due to its slow growth and sedentary adults. Two hypotheses are considered in this study, the first being that the eggs and larvae remain in the habitats where the adults are found and this would lead to less gene flow between geographically separated habitats (hypothesis of isolation). Alternatively the eggs and larvae could be transported by the inshore currents which would lead to a single population identified along the west coast of South Africa (hypothesis of panmixia). The main aim of this study was to investigate which of these two hypotheses best explains the population connectivity in the hottentot seabream.

For this purpose, the spatial and temporal genetic variation of this species along the South African west coast was assessed. Fourteen highly polymorphic loci were genotyped for 288 individuals across nine locations sampled in 2001 and in 189 samples from six locations in 2009 (Fig. 2). Individual-based statistical analyses suggested the presence of one population along the coast. The effective population size was estimated to be relatively small (~ 9989 individuals). Weak spatial structure was identified between the sampling locations from 2009 using Factorial Correspondence Analysis (FCA), Analysis of Molecular Variance (AMOVA) and Spatial Autocorrelation (SAC). Between the 2001 sampling locations no significant spatial structure was identified. Temporal variation was identified between the two sampling years. This was likely due to “larval genetic patchiness” which led to variations in the observed population structure across different years. In conclusion, one population of the hottentot seabream was identified along the coast of South Africa with weak spatial and temporal variation between years, which is likely due to the larval dispersal and mortality mediated through the oceanographic features along the west coast.

Fig. 2 Map of the locations sampled along the coast of South Africa in 2001 and 2009. The 2001 sampling locations are indicated in blue and the 2009 sampling locations in red. The inset shows a map of Africa (google maps; orange line indicates the west coast of southern Africa where the hottentot is distributed) and an image of the hottentot seabream.

Introgressive hybridization in herring gulls

Next Monday, Paulette will present a paper on the evolutionary history of three closely related species of Herring Gull: Larus argenteus, L. hyperboreus, L. marinus. A previous study showed that each of these species presented a biphyletic pattern based on mitochondrial markers, suggesting introgression events provoked by recent hybridization. In this paper, the authors studied the evolutionary history of these species, specifically analyzing the introgression events using both mtDNA and RLFP. Thanks Paulette.

From Sternkopf V, Liebers-Helbig D, Ritz MS, Zhang J, Helbig AJ, de Knijff P (2010) BMC Evolutionary Biology 10:348

Title: Introgressive hybridization and the evolutionary history of the herring gull complex revealed by mitochondrial and nuclear DNA

Abstract

Background: Based on extensive mitochondrial DNA (mtDNA) sequence data, we previously showed that the model of speciation among species of herring gull (Larus argentatus) complex was not that of a ring species, but most likely due more complex speciation scenario’s. We also found that two species, herring gull and glaucous gull (L. hyperboreus) displayed an unexpected biphyletic distribution of their mtDNA haplotypes. It was evident that mtDNA sequence data alone were far from sufficient to obtain a more accurate and detailed insight into the demographic processes that underlie speciation of this complex, and that extensive autosomal genetic analysis was warranted.

Results: For this reason, the present study focuses on the reconstruction of the phylogeographic history of a limited number of gull species by means of a combined approach of mtDNA sequence data and 230 autosomal amplified fragment length polymorphism (AFLP) loci. At the species level, the mtDNA and AFLP genetic data were largely congruent. Not only for argentatus and  hyperboreus, but also among a third species, great black-backed gull (L. marinus) we observed two distinct groups of mtDNA sequence haplotypes. Based on the AFLP data we were also able to detect distinct genetic subgroups among the various argentatus, hyperboreus, and marinus populations, supporting our initial hypothesis that complex demographic scenario’s underlie speciation in the herring gull complex.

Conclusions: We present evidence that for each of these three biphyletic gull species, extensive mtDNA introgression could have taken place among the various geographically distinct subpopulations, or even among current species. Moreover, based on a large number of autosomal AFLP loci, we found evidence for distinct and complex demographic scenario’s for each of the three species we studied. A more refined insight into the exact phylogeographic history within the herring gull complex is still impossible, and requires detailed autosomal sequence information, a topic of our future studies.

Global Phylogeography of Angel sharks

Next Monday, Madonna will present a paper on phylogeny and global phylogeography of Angel sharks: 17 (out of 22) species in the genus Squatina. In this paper, the authors first obtained a comprehensive phylogenetic reconstruction and tested biogeographic patterns using a molecular clock. The genus was found to be monophyletic and composed of four main clades. The authors found supports for the effect of both the Thetys Sea closure and the rise of the Panamian isthmus on the diversification of the genus. Thanks Madonna.

From Stelbrink B, vonRintelen T, Cliff G, Kriwet J; Molecular Phylogenetic and Evolution (2010) 54:395-404

Title: Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Abstract.

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe–North Africa–Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.

Phylogeography of Dalton's Mouse (West Africa)

Next Monday, Catherine will present a paper on phylogeography of a small rodent: the Dalton's Mouse in West Africa. In this paper, the authors (1) found discrepancies between recognized morphospecies and phylogenetic results, (2) found evidence of refuges in the region, (3) found an effect of biogeographic barriers, (4) discussed the taxonomic status (biological species) of the different lineages and (5) found support for historic introgression events between lineages. Thanks Catherine.

From J. BRYJA, L. GRANJON, G. DOBIGNY, H. PATZENHAUEROVA, A. KONECNY, J.M. DUPLANTIER, P. GAUTHIER, M. COLYN, L. DURNEZ, A. LALIS and V. NICOLAS; Molecular Ecology (2010) doi: 10.1111/j.1365-294X.2010.04847.x

Title: Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay

Abstract.

Rodents of the Praomys daltoni complex are typical inhabitants of the Sudanian savanna ecosystem in western Africa and represent a suitable model for testing the effect s of Quaternary climatic oscillations on extant genetic variation patterns. Phylogeographical analyses of mitochondrial DNA sequences (cytochrome b) across the distribution range of the complex revealed several well-defined clades that do not support the division of the clade into the two species currently recognized on the basis of morphology, i.e. P. daltoni (Thomas, 1892) and Praomys derooi (Van der Straeten & Verheyen 1978). The observed genetic structure fits the refuge hypothesis, suggesting that only a small number of populations repeatedly survived in distinct forest-savanna mosaic blocks during the arid phases of the Pleistocene, and then expanded again during moister periods. West African rivers may also have contributed to genetic differentiation, especially by forming barriers after secondary contact of expanding populations. The combination of three types of genetic markers (mtDNA sequences, microsatellite loci, cytogenetic data) provides evidence for the presence of up to three lineages, which most probably represent distinct biological species. Furthermore, incongruence between nuclear and mtDNA markers in some individuals unambiguously points towards a past introgression event. Our results highlight the importance of combining different molecular markers for an accurate interpretation of genetic data.

Phylogeography of poison frog

Next Monday, Samantha will present a paper on phylogeography of poison frog in Costa Rica and Panama. In this paper, the authors try to identify the level of mitochondrial polyphyly within the species (though I don’t really understand what that means). The second aim is to identify the phylogeographic pattern of this species on its distribution range and compare it to other frogs in the same region. Find below the details of the study. Thanks Samantha.

From J. Susanne Hauswaldt, Ann-Kathrin Ludewig, Miguel Vences and Heike Prohl, Journal of Biogeography (2010) doi:10.1111/j.1365-2699.2010.02438.x

Title: Widespread co-occurrence of divergent mitochondrial haplotype lineages in a Central American species of poison frog (Oophaga pumilio)

Abstract.

Aim To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers.

Location Costa Rica and Panama.

Methods Sequence analyses of a mitochondrial (cytochrome b) and a nuclear (RAG-1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei.

Results Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co-occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the ‘southern lineage’ shifted this barrier towards the

north.

Main conclusions Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus.

What is a species tree?

Because I maybe expected a lot from the last journal club (Brunes et al. 2010) for us to understand the concept of Species tree, I was a bit disappointed. So, I googled this morning to search for some answers. I found some, though not many. So, you can find below the two sources where I found definitions for "Species tree". Then, I propose a tentative definition and try to cover all the implications I could find when attempting to resolve a species tree. Hope it will help!

Sources:

www.encyclopedia.com

species tree: A phylogenetic tree which depicts the evolutionary relationships of a set of species. Inferred trees, based on gene trees or other character trees, are often presented as estimates of the true species tree.

www.nature.com/nrmicro/journal/v1/n2/glossary/nrmicro751_glossary.html

A phylogenetic tree that represents evolutionary relationships between species as a whole, as opposed to phylogenetic trees for individual genes

A tentative definition of Species tree:

“Species tree” is the conceptual view of the real evolutionary relationships between species. It is opposed to the phylogenetic trees drew from individual genes that give potentially different evolutionary relationships between species.

What does it mean:

I think that the basis of this concept reside in the fact that the evolutionary relationships constructed from individual genes are false in general, maybe very false compared to the species tree. To resolve a species tree, the alternative is to use several or numerous genes (depending on the model), expecting to find a great improvement in the resolution of the tree. I think one can find an ultimate resolution of the species tree if and only if one can find concordant evolutionary relationships between species using different sets of genes. Probably, sometimes it is possible, sometimes not. So, as we saw in this paper of Brunes et al. (2010), finding supports for the different nodes using several genes allowed them to reach the species tree of these tree frogs. I guess the worse cases would be those involving radiations where no support could be found because the relationships between the species represent a polytomy (all lineages diverged at the same time). In such cases, I guess people would keep trying to add more and more genes without getting any concordant resolution.